I was lucky to have a working Mac LC 630 available; I just hooked it up to its scsi port (externally), waited for it to finally calibrate and backed it up/formatted it from that machine. If you need to format the drive in the SE it may help to create or ask someone for a macOS 6.0.x floppy with...
Probably the drive is trying to align / calibrate it’s heads, I had the same issue with the drive in my Mac SE. A low level format fixed the issue for me.
Try to switch the SE on while holding down the mouse button; my Radius accelerator shows the following screen (from its ROM) where you can disable the accelerator or it’s caches:
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